Blender for dental treatment planning?
I don't know how well this question can be answered, but I'll give it a shot.

1. I believe the difficulty of separating out individual teeth depends on:


The quality of your scan data
Your modeling skills
Your knowledge of anatomy
Any additional data you may have to reference (x-rays?)


In the 3D scan there is no differentiation between tooth and bone, so you have to recreate it. Taking x-ray images to accompany your 3D scan data may help significantly by letting you see where one ends and the other begins - and ideally you will want at least a front and a side view.

2. This is an extension of the idea in Part 1. Filling holes is easy, as far as modeling goes. The accuracy however, will depend on the data you have available and your abilities. 

3. I'm not clear on what you mean by "3D matrix". 3D coordinate data is always represented as a matrix, but I don't think that's what you mean here. In any case there are many ways to present your 3D models in Blender, including using animation. If you describe what you mean in more detail I can probably address this point better.

4. You can use Blend4Web to embed your Blender scenes in a web page. Since it does not require any browser plug-ins anyone can view it, even on mobile devices. The details of how to do this are beyond the scope of this question, but you can learn about it on the Blend4Web site.

Here is a related dental modeling question worth looking at.

The link in Abel's comment looks promising as well, although I'm not familiar with it.

Good luck and please let us know how it works out.